The whole premise of MOS was that this was a gritty, realistic world before Superman showed up. There was no room for Superman in the Batman stories that Nolan told, but now that they've been told, the alien has arrived and the world has changed.

You could just as easily say that there was no room for Thor and an alien invasion in Iron Man's universe...but it happened.

Yeah, you can have an escalation of superhero elements within the Nolanverse, but they'll probably introduce a new Batman and establish that Man of Steel isn't in the same universe as Nolan's Batman trilogy as that would give them the freedom to do whatever they want with future Batman movies in terms of the Joker and so forth.